updated various functions for comapibility with modern R (R 4.3.x, tidytable_0.10.2)
epitopefindr 1.1.30 (2020-09-19)
Minor changes
Keep blast alignment table as data.table::data.table to fix changes in R 4.0
changed pdf merge default to pdfuniter to get around rJava issue
epitopefindr 1.1.29 (2020-05-30)
Minor changes
Specify remote sources for Bioconductor and Github package dependencies.
epitopefindr 1.1.28 (2020-05-07)
Minor changes
multiple sequence alignment consensus sequence defaults changed. Consensus sequence type = “upperlower”, thresh = c(100, 50). See ?msa::msaConsensusSequence for more information.
epitopefindr 1.1.27 (2020-05-06)
Minor changes
epitopeSummary output table sorting modification. group number coerced to numeric.
epitopefindr 1.1.26
Breaking changes
output table changes (fixed bug with epitope_summary$id number of rows mismatch, outputTable() function now returns a list with epitope_key and epitope_summary tables as elements, epfind() writes csvs with “NA” to fill empty cells)
Minor changes
added parameter remove.intermediates = FALSE to epfind(). If set to true, then the /intermediate_files/ folder is deleted from epitopefindr’s output directory at the end of the run.
epitopefindr 1.1.25
Minor changes
Added support for command line utility pdfunite as an alternative to pdftk.